Hi @Mehrbod_Estaki,
Thank you! I copied only the required cells and past them in new sheet to use it.
With Phred33 it is working but error shows with Phred64
qiime tools import \
> --type 'SampleData[PairedEndSequencesWithQuality]' \
> --input-path cleaned_rename_28w_manifest.csv \
> --output-path w28_Ph64_paired-end-demux.qza \
> --source-format PairedEndFastqManifestPhred64
/Users/faisal/miniconda2/envs/qiime2-2018.4/lib/python3.5/site-packages/q2_types/per_sample_sequences/_transformer.py:344: UserWarning: Importing of PHRED 64 data is slow as it is converted internally to PHRED 33. Working with the imported data will not be slower than working with PHRED 33 data.
warnings.warn(_phred64_warning)
/Users/faisal/miniconda2/envs/qiime2-2018.4/lib/python3.5/site-packages/skbio/io/registry.py:557: ArgumentOverrideWarning: Best guess was: variant='illumina1.8', continuing with user supplied: 'illumina1.3'
ArgumentOverrideWarning)
Traceback (most recent call last):
File "/Users/faisal/miniconda2/envs/qiime2-2018.4/lib/python3.5/site-packages/q2cli/tools.py", line 116, in import_data
view_type=source_format)
File "/Users/faisal/miniconda2/envs/qiime2-2018.4/lib/python3.5/site-packages/qiime2/sdk/result.py", line 218, in import_data
return cls._from_view(type_, view, view_type, provenance_capture)
File "/Users/faisal/miniconda2/envs/qiime2-2018.4/lib/python3.5/site-packages/qiime2/sdk/result.py", line 243, in _from_view
result = transformation(view)
File "/Users/faisal/miniconda2/envs/qiime2-2018.4/lib/python3.5/site-packages/qiime2/core/transform.py", line 70, in transformation
new_view = transformer(view)
File "/Users/faisal/miniconda2/envs/qiime2-2018.4/lib/python3.5/site-packages/q2_types/per_sample_sequences/_transformer.py", line 346, in _9
single_end=False)
File "/Users/faisal/miniconda2/envs/qiime2-2018.4/lib/python3.5/site-packages/q2_types/per_sample_sequences/_transformer.py", line 288, in _fastq_manifest_helper
fastq_copy_fn(input_fastq_fp, str(output_fastq_fp))
File "/Users/faisal/miniconda2/envs/qiime2-2018.4/lib/python3.5/site-packages/q2_types/per_sample_sequences/_transformer.py", line 313, in _write_phred64_to_phred33
variant='illumina1.3'):
File "/Users/faisal/miniconda2/envs/qiime2-2018.4/lib/python3.5/site-packages/skbio/io/registry.py", line 1161, in read
**kwargs)
File "/Users/faisal/miniconda2/envs/qiime2-2018.4/lib/python3.5/site-packages/skbio/io/registry.py", line 506, in read
return (x for x in itertools.chain([next(gen)], gen))
File "/Users/faisal/miniconda2/envs/qiime2-2018.4/lib/python3.5/site-packages/skbio/io/registry.py", line 531, in _read_gen
yield from reader(file, **kwargs)
File "/Users/faisal/miniconda2/envs/qiime2-2018.4/lib/python3.5/site-packages/skbio/io/registry.py", line 1008, in wrapped_reader
yield from reader_function(fhs[-1], **kwargs)
File "/Users/faisal/miniconda2/envs/qiime2-2018.4/lib/python3.5/site-packages/skbio/io/format/fastq.py", line 354, in _fastq_to_generator
qual_header)
File "/Users/faisal/miniconda2/envs/qiime2-2018.4/lib/python3.5/site-packages/skbio/io/format/fastq.py", line 523, in _parse_quality_scores
phred_offset=phred_offset))
File "/Users/faisal/miniconda2/envs/qiime2-2018.4/lib/python3.5/site-packages/skbio/io/format/_base.py", line 34, in _decode_qual_to_phred
% (phred_range[0], phred_range[1]))
ValueError: Decoded Phred score is out of range [0, 62].
An unexpected error has occurred:
Decoded Phred score is out of range [0, 62].
See above for debug info.
I’m not sure which Phred I have for my data. But at least I’m glad it is imported with Phred33 at least.
Thanks!